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An Oceanside boy missing for two days was found safe on June 26, 2014. However, instead of being reunited with his family, he was taken into protective custody. NBC 7's Danya Bacchus reports on the latest developments in this story. (Published Friday, June 27, 2014)

A 13-year old Oceanside, California, boy who may have set out on his own Tom Sawyer-inspired journey was found safe Thursday — but in a twist to the tale, the boy was not reunited with his family but instead placed in protective custody.

The young teen had been reported missing by his mother early Wednesday morning after she was unable to find him at home. The mother told officials she had last seen her son Tuesday around 10 p.m. and a search for the boy ensued.

His mother told NBC 7 her son was a fan of Mark Twain's "The Adventures of Tom Sawyer," so he may have been inspired by the main character to take a journey of his own.

She said he had taken a survival kit with him that he recently bought at the fair, as well as a backpack.

At around 7:30 p.m. Thursday, the boy's mother received a call saying her son had been found.

However, as she waited for police to bring him home, she found out he wouldn't be coming back – at least not for now.

Oceanside police said the boy and his 14-year-old brother had been placed in protective custody based on some unspecified information they received during the course of their search and investigation.

Since the investigation is ongoing, police said they could not elaborate on what led them to make that decision.

Three other siblings were allowed to remain in the family's home, officials said.

Throughout Thursday, the San Diego County Sheriff's Department's Search and Rescue Team canvassed the boy's neighborhood at Concho Place near the San Luis Rey Riverbed and Camp Pendleton with a search dog.

The boy wasn't found near his home, but instead was found hiding in bushes off El Camino Real and Vista Rey. Police said he was safe and in good condition.

Police initially said the boy was taken into custody to find out what he was doing and what prompted him to run away. However, further details were not released.